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Dear Douglos,

I did not understand how to use mri_label2label with the mask option(there is srcmask options not mask alone !). I extract my labels and as you explained I wanted to create i.e. binary mask of rh.fusiform.label  with mri_label2label :
  mri_label2label  --srcsubject case1 --srclabel rh.fusiform.label --trgsubject case1 --trglabel outputlabel.mgh --regmethod surface --hemi rh

but it creats another label file not binary with mgh format I did not get how can I create mybinary.mgh mask in order to use in third command "mri_binarize --i lh.thickness --mask youmask.mgh --o lh.thickness.masked.mgh"

would you please help me with this, it would be a great favor.

Best regards,
Nazanin

On Mon, Jul 30, 2018 at 10:59 PM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:
Yes, that should work. You can create a mask by breaking the annotation
into labels (mri_annotation2label), then converting the label into a
binary mask (mri_label2label with --mask option), then mri_binarize --i
lh.thickness --mask youmask.mgh --o lh.thickness.masked.mgh


On 07/30/2018 01:47 AM, N Saf wrote:
>
>         External Email - Use Caution
>
> Dear Freesurfer Experts,
>
> I wonder how can I show the cortical thickness surface on just one
> region of my interest in Freeview.  assume that I want to see the
> thickness surface of one of the regions in DKTatlas. does it work if I
> make a binary mask of that specific region on aparcDKTatlas.annot and
> then multiply it to the ?h.thickness surface ?? any help will be
> appreciated.
>
> Best Regards,
> Nazanin
>
>
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